Hi, I am developing a package for Bioconductor, and I have a weird issue when importing the 'methods' package. Before I add the 'methods' package in Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings.
However, when I add the 'methods' package in the Imports field, I get a warning during CMD check. (I need the methods package since I use the methods::is() function, and if I call it just as is(), when running the package from Rscript will fail since by default it does not load the 'methods' package.) I read a similar issue here: https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html and I updated all my packages from Bioconductor including IRanges and GenomicRanges. This is the warning that I get, which is exactly the same as the previous issue in Bioc-Devel, and I understand that for some reason the BiocGenerics is attached only when the 'methods' package is imported. * checking for missing documentation entries ... WARNING Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. My DESCRIPTION file when I add the 'methods' package is the following: ... Depends: R (>= 3.2.0) LazyData: TRUE RoxygenNote: 5.0.1 Imports: GenomicRanges, IRanges, assertthat, S4Vectors, graphics, data.table, methods Suggests: knitr, rmarkdown, testthat VignetteBuilder: knitr Regards, Andreas [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel